title: Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species.
abstract: Foxtail millet (Setariaitalica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02-0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.
authors.affiliation: National Institute of Plant Genome Research, New Delhi, India.
authors.forename: Kajal
authors.initials: K
authors.lastname: Kumari
authors.forename: Mehanathan
authors.initials: M
authors.lastname: Muthamilarasan
authors.forename: Gopal
authors.initials: G
authors.lastname: Misra
authors.forename: Sarika
authors.initials: S
authors.lastname: Gupta
authors.forename: Alagesan
authors.initials: A
authors.lastname: Subramanian
authors.forename: Swarup Kumar
authors.initials: SK
authors.lastname: Parida
authors.forename: Debasis
authors.initials: D
authors.lastname: Chattopadhyay
authors.forename: Manoj
authors.initials: M
authors.lastname: Prasad
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000378:metabolism; D018744:DNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D014644:Genetic Variation; D018895:Microsatellite Repeats / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D012639:Seeds / Q000033:anatomy & histology; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D032983:Setaria Plant / Q000145:classification / Q000235:genetics*; D045868:Sorghum / Q000235:genetics; D003313:Zea mays / Q000235:genetics
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers